Reconstruction of genome-scale metabolic models of non-conventional yeasts: current state, challenges, and perspectives

IF 2.5 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Eduardo Luís Menezes de Almeida, Eduard J. Kerkhoven, Wendel Batista da Silveira
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引用次数: 0

Abstract

Non-conventional yeasts are promising cell factories to produce lipids and oleochemicals, metabolites of industrial interest (e.g., organics acids, esters, and alcohols), and enzymes. They can also use different agro-industrial by-products as substrates within the context of a circular economy. Some of these yeasts can also comprise economic and health burdens as pathogens. Genome-scale metabolic models (GEMs), networks reconstructed based on the genomic and metabolic information of one or more organisms, are great tools to understand metabolic functions and landscapes, as well as propose engineering targets to improve metabolite production or propose novel drug targets. Previous reviews on yeast GEMs have mainly focused on the history and the evaluation of Saccharomyces cerevisiae modeling paradigms or the accessibility and usability of yeast GEMs. However, they did not describe the reconstruction strategies, limitations, validations, challenges, and research gaps of non-conventional yeast GEMs. Herein, we focused on the reconstruction of available non-Saccharomyces GEMs, their validation, underscoring the physiological insights, as well as the identification of both metabolic engineering and drug targets. We also discuss the challenges and knowledge gaps and propose strategies to boost their use and novel reconstructions.

Abstract Image

非常规酵母菌基因组尺度代谢模型的重建:现状、挑战和前景
非常规酵母是生产脂类和油脂化学品、工业用代谢物(如有机酸、酯和醇)以及酶的有前途的细胞工厂。在循环经济的背景下,它们还可以利用不同的农用工业副产品作为基质。其中一些酵母菌还可以作为病原体造成经济和健康负担。基因组尺度代谢模型(GEM)是根据一个或多个生物体的基因组和代谢信息重建的网络,是了解代谢功能和代谢景观的重要工具,也是提出工程目标以改善代谢物生产或提出新型药物靶点的重要工具。以往关于酵母 GEM 的综述主要集中在酵母建模范式的历史和评估,或酵母 GEM 的可及性和可用性。然而,它们并没有描述非常规酵母 GEM 的重建策略、局限性、验证、挑战和研究空白。在本文中,我们重点讨论了现有非酵母 GEMs 的重建、验证、生理学见解以及代谢工程和药物靶点的鉴定。我们还讨论了所面临的挑战和知识差距,并提出了促进其使用和新型重建的策略。
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来源期刊
Biotechnology and Bioprocess Engineering
Biotechnology and Bioprocess Engineering 工程技术-生物工程与应用微生物
CiteScore
5.00
自引率
12.50%
发文量
79
审稿时长
3 months
期刊介绍: Biotechnology and Bioprocess Engineering is an international bimonthly journal published by the Korean Society for Biotechnology and Bioengineering. BBE is devoted to the advancement in science and technology in the wide area of biotechnology, bioengineering, and (bio)medical engineering. This includes but is not limited to applied molecular and cell biology, engineered biocatalysis and biotransformation, metabolic engineering and systems biology, bioseparation and bioprocess engineering, cell culture technology, environmental and food biotechnology, pharmaceutics and biopharmaceutics, biomaterials engineering, nanobiotechnology, and biosensor and bioelectronics.
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